NPASS Compound

Natural Product: NPC5107

Natural Product ID	NPC5107
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	UBVTXRWIGGYYPO-KSSFIOAISA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	53359579
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0001969] Dibenzylbutane lignans

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 60 61 0 0 0 0 0 0 0 0999 V2000 -1.3900 1.9044 0.2016 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8811 0.5605 0.7031 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8319 -0.5253 0.2412 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1962 -0.2647 0.7714 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5979 -0.7567 2.0183 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8626 -0.5195 2.4991 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7400 0.2105 1.7421 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3904 0.7172 0.5055 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0976 0.4576 0.0471 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3236 1.4464 -0.2083 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0766 2.0031 -1.4650 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0110 0.4426 2.2374 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5448 0.2879 0.3062 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9648 -1.0506 0.8769 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3971 -1.3560 0.5203 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4499 -0.9635 1.2964 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7762 -1.2596 0.9600 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9890 -1.9731 -0.2011 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9543 -2.3880 -1.0124 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6547 -2.0673 -0.6320 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2460 -3.0995 -2.1608 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1629 -3.5155 -2.9794 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3317 -2.2541 -0.5104 O 0 0 0 0 0 0 0 0 0 0 0 0 5.7997 -0.8324 1.7904 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6130 -0.1124 2.9656 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7287 0.2563 -1.1909 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4061 1.4605 -1.8226 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0932 2.6361 -1.5756 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0513 2.6949 -0.7689 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7116 3.8966 -2.2724 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7353 2.7028 0.5803 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3809 2.0451 0.7291 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6194 1.9261 -0.8625 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9602 0.5906 1.8089 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5767 -1.5335 0.5963 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8280 -0.5755 -0.8723 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8435 -1.3275 2.5595 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1603 -0.8962 3.4464 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8374 0.8600 -0.9218 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0439 2.2220 -1.9771 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4840 1.3553 -2.1401 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5633 2.9832 -1.3615 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7611 -0.1746 1.9489 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2096 1.1023 0.6854 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3127 -1.8212 0.4429 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8915 -1.0134 1.9583 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2416 -0.4069 2.1971 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8701 -2.4124 -1.2978 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4045 -4.0929 -2.4249 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5092 -4.1642 -3.8141 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6550 -2.6138 -3.4038 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6877 -3.1324 -0.1231 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5733 0.2339 3.3729 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1751 -0.8133 3.7208 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9182 0.7418 2.7696 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1760 -0.6094 -1.6373 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8313 0.0979 -1.3890 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4460 4.7064 -1.5847 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5506 4.2692 -2.9147 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1344 3.7141 -2.9746 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 2 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 2 0 8 10 1 0 10 11 1 0 7 12 1 0 2 13 1 0 13 14 1 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 2 0 19 21 1 0 21 22 1 0 18 23 1 0 17 24 1 0 24 25 1 0 13 26 1 0 26 27 1 0 27 28 1 0 28 29 2 0 28 30 1 0 9 4 1 0 20 15 1 0 1 31 1 0 1 32 1 0 1 33 1 0 2 34 1 1 3 35 1 0 3 36 1 0 5 37 1 0 6 38 1 0 9 39 1 0 11 40 1 0 11 41 1 0 11 42 1 0 12 43 1 0 13 44 1 1 14 45 1 0 14 46 1 0 16 47 1 0 20 48 1 0 22 49 1 0 22 50 1 0 22 51 1 0 23 52 1 0 25 53 1 0 25 54 1 0 25 55 1 0 26 56 1 0 26 57 1 0 30 58 1 0 30 59 1 0 30 60 1 0 M END

Standard InCHIKey	UBVTXRWIGGYYPO-KSSFIOAISA-N
Standard InCHI	InChI=1S/C23H30O7/c1-14(8-16-6-7-19(25)20(10-16)27-3)18(13-30-15(2)24)9-17-11-21(28-4)23(26)22(12-17)29-5/h6-7,10-12,14,18,25-26H,8-9,13H2,1-5H3/t14-,18-/m0/s1
SMILES	C[C@@H](Cc1ccc(c(c1)OC)O)[C@@H](Cc1cc(c(c(c1)OC)O)OC)COC(=O)C

Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO2462	Machilus robusta	Species	Lauraceae	Eukaryota	bark	n.a.	n.a.	PMID[21627109]
NPO2462	Machilus robusta	Species	Lauraceae	Eukaryota	n.a.	bark	n.a.	PMID[21627109]
NPO2462	Machilus robusta	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO2462	Machilus robusta	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	Organism Name	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC5107 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	14129
0.1-0.2	29935
0.2-0.3	5070
0.3-0.4	523
0.4-0.5	132
0.5-0.6	43
0.6-0.7	19
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9149	High Similarity	NPC487680
0.7544	Intermediate Similarity	NPC487679
0.7544	Intermediate Similarity	NPC487678
0.7407	Intermediate Similarity	NPC273657
0.6667	Remote Similarity	NPC68779
0.6667	Remote Similarity	NPC108598
0.6333	Remote Similarity	NPC67247
0.6275	Remote Similarity	NPC31344
0.6275	Remote Similarity	NPC317769
0.6271	Remote Similarity	NPC106920
0.6271	Remote Similarity	NPC15811
0.625	Remote Similarity	NPC165133
0.625	Remote Similarity	NPC242885
0.625	Remote Similarity	NPC95614
0.625	Remote Similarity	NPC232316
0.6167	Remote Similarity	NPC606339
0.6066	Remote Similarity	NPC610284
0.6	Remote Similarity	NPC110699
0.6	Remote Similarity	NPC300776
0.6	Remote Similarity	NPC176814
0.6	Remote Similarity	NPC4982
0.6	Remote Similarity	NPC106055
0.6	Remote Similarity	NPC606629
0.5862	Remote Similarity	NPC275950
0.5806	Remote Similarity	NPC485282
0.5806	Remote Similarity	NPC485283
0.5806	Remote Similarity	NPC485281
0.5781	Remote Similarity	NPC282291
0.5781	Remote Similarity	NPC166137
0.5741	Remote Similarity	NPC227217
0.5741	Remote Similarity	NPC117780
0.5692	Remote Similarity	NPC216223
0.5645	Remote Similarity	NPC486558
0.5556	Remote Similarity	NPC56214
0.5556	Remote Similarity	NPC487676
0.5538	Remote Similarity	NPC608199
0.5517	Remote Similarity	NPC274356
0.5517	Remote Similarity	NPC173308
0.5517	Remote Similarity	NPC181079
0.5517	Remote Similarity	NPC101748
0.55	Remote Similarity	NPC253481
0.55	Remote Similarity	NPC253722
0.55	Remote Similarity	NPC475875
0.5469	Remote Similarity	NPC145569
0.5455	Remote Similarity	NPC120852
0.5397	Remote Similarity	NPC100675
0.5397	Remote Similarity	NPC282833
0.5397	Remote Similarity	NPC476345
0.5397	Remote Similarity	NPC601691
0.5373	Remote Similarity	NPC281780
0.5357	Remote Similarity	NPC127587
0.5323	Remote Similarity	NPC102908
0.5294	Remote Similarity	NPC193544
0.5217	Remote Similarity	NPC478703
0.5217	Remote Similarity	NPC478704
0.5211	Remote Similarity	NPC252402
0.5211	Remote Similarity	NPC102934
0.5156	Remote Similarity	NPC90431
0.5102	Remote Similarity	NPC156840
0.5094	Remote Similarity	NPC85488
0.5094	Remote Similarity	NPC603326
0.5079	Remote Similarity	NPC187998
0.5079	Remote Similarity	NPC257582
0.5079	Remote Similarity	NPC241522
0.5075	Remote Similarity	NPC471988
0.5075	Remote Similarity	NPC169973

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC5107 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3024
0.1-0.2	5780
0.2-0.3	334
0.3-0.4	10
0.4-0.5	2
0.5-0.6	0
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
		NPD

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data